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The main readme file and the bash help files for all executables in /bin are the primary documentation for informME. This wiki is aimed at being a gentle introduction to the software with example usage, but the help files in the code are the gold-standard documentation of informME.
Community contributions to the code or documentation are warmly welcomed.
If you use informME, please cite:
[1] Jenkinson, G., Pujadas, E., Goutsias, J., and Feinberg, A.P. (2017), Potential energy landscapes identify the information-theoretic nature of the epigenome, Nature Genetics, 49: 719-729.
[2] Jenkinson, G., Abante, J., Feinberg, A.P., and Goutsias, J. (2018), An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data, BMC Bioinformatics, 19:87, https://doi.org/10.1186/s12859-018-2086-5.
[3] Jenkinson, G., Abante, J., Koldobskiy, M., Feinberg, A.P., and Goutsias, J. (2019), Ranking genomic features using an information-theoretic measure of epigenetic discordance, BMC Bioinformatics, 20:175, https://doi.org/10.1186/s12859-019-2777-6.
- Home
- Software Overview
- Dependencies
- Installing InformME
- Directory Structure
- Usage
- Reference Genome Analysis
- Methylation Data Matrix Generation
- Model Estimation & Analysis
- Generate BEDGRAPH Files for Single Analysis
- Generate BEDGRAPH Files for Differential Analysis
- Postprocessing: BEDGRAPH to BW Conversion
- Postprocessing: DMR Detection
- Postprocessing: Gene Ranking
- Testing/Debugging Your Install
- FAQs
- Version History
- Licencing